In general the Lakes are quite shallow, ranging from about 20m to 40m (65ft to 131ft). However, there are three deep basins that are well over 100m (328ft). The deepest is in the form of a long trench at the bottom of St. Andrews Channel which reaches 280m (918ft).

Compared to the total volume of water in the Lakes the input from rivers is very small. If the Lakes were empty, it would take 7 years to fill them with river water. Fresh water stays mostly on the surface and leaves the Lakes through the Great Bras d'Or Channel. This low salinity water is replaced by much saltier water flowing in along the bottom from Sydney Bight.

The average salinity is about 22 parts per thousand (o/oo). By comparison, Sydney Bight is around 28 to 30 o/oo; the Atlantic ocean ranges from 32 to 37 o/oo. The water in the Lakes is much saltier at depth than at the surface because of inflow of freshwater from rivers. The total amount of salt in the Bras d'Or Lakes is about 700 million tons.

Artificial structures can form a good substrate for marine creatures both sessile and free-living to inhabit, in fact a number of concrete structures have been placed in the Lakes as habitat for lobsters by the Department of Fisheries and Oceans and the Eskasoni Fish and Wildlife Commission . However, sinking ships is another matter. A thorough cleaning to remove pollutants is necessary and very expensive if done properly. Even then, it is impossible to remove all noxious materials from pipes and inacessible corners of bilges. In the open ocean, tides and currents will remove and quickly dilute these residual toxic materials with little consequence. However, the Bras d'Or Lakes would be particularly vulnerable as there is very low flushing of waters. For instance, a complete exchange of water within Whycocomagh Bay would take well over two years, and St. Andrews Channel, about 1 year. The fastest flushing rates would be near the entrance to the Lakes in the Great Bras d'Or Channel where it would be less than a week.
Many marine biologists and oceanographers have raised concerns with this practice and Japan and California have banned sinking of ships for artificial reefs.